Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole,Solea Solea

Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using DNA marker data. With missing parents and natural mating groups, commonly used pedigree reconstruction methods are not accurate and lead to loss of data. Relatedness estimators, however, infer relationships between all animals sampled. In this study, we compared a pedigree relatedness method and a relatedness estimator (“molecular relatedness”) method using accuracy of estimated breeding values. A commercial data set of common sole, Solea solea, with 51 parents and 1953 offspring (“full data set”) was used. Due to missing parents, for 1338 offspring, a pedigree could be reconstructed with 10 microsatellite markers (“reduced data set”). Cross-validation of both methods using the reduced data set showed an accuracy of estimated breeding values of 0.54 with pedigree reconstruction and 0.55 with molecular relatedness. Accuracy of estimated breeding values increased to 0.60 when applying molecular relatedness to the full data set. Our results indicate that pedigree reconstruction and molecular relatedness predict breeding values equally well in a population with skewed contributions to families. This is probably due to the presence of few large full-sib families. However, unlike methods with pedigree reconstruction, molecular relatedness methods ensure availability of all genotyped selection candidates, which results in higher accuracy of breeding value estimation.To estimate genetic parameters, additive genetic relationships between individuals are inferred from known pedigrees (Falconer and Mackay 1996; Lynch and Walsh 1997). However, in natural populations (Ritland 2000; Thomas et al. 2002) and in captive species where natural mating in groups is used to obtain offspring (Brown et al. 2005; Fessehaye et al. 2006; Blonk et al. 2009) pedigrees are reconstructed. In these populations there is no control on mating structure, and typically unbalanced population structures with highly skewed parental contributions are obtained (Bekkevold et al. 2002; Brown et al. 2005; Fessehaye et al. 2006; Blonk et al. 2009). To reconstruct pedigrees, parental allocation methods are often used (Marshall et al. 1998; Avise et al. 2002; Duchesne et al. 2002). These methods require that all parents be known. For situations where parental information is not available, numerous DNA-marker-based methods for estimating molecular relatedness have been developed (Lynch 1988; Queller and Goodnight 1989; Ritland 2000; Toro et al. 2002). These relatedness estimators determine relationship values between individuals on a continuous scale. Evaluation of relatedness estimators within real and simulated data in both plants and animals (e.g., see Van de Casteele et al. 2001 ; Milligan 2003; Oliehoek et al. 2006; Rodríguez-Ramilo et al. 2007; Bink et al. 2008) has generally focused on bias and sampling error of estimated genetic variances or relatedness values. Relatively little attention has been paid to their efficiency for estimation of breeding values.Two types of relatedness estimators are currently available: method-of-moments estimators and maximum-likelihood estimators. Method-of-moments estimators (e.g., Queller and Goodnight 1989; Li et al. 1993; Ritland 1996; Lynch and Ritland 1999; Toro et al. 2002) determine relationships while calculating sharing of alleles between pairs in different ways. A variant of method-of-moments estimators is the transformation of continuous relatedness values to categorical genealogical relationships using “explicit pedigree reconstruction” (Fernández and Toro 2006) or thresholds (Rodríguez-Ramilo et al. 2007). However, correlations of transformed coancestries with known genealogical coancestries are low (Rodríguez-Ramilo et al. 2007). Several studies have compared different method-of-moments estimators but none revealed one single best estimator (Van de Casteele et al. 2001; Oliehoek et al. 2006; Rodríguez-Ramilo et al. 2007; Bink et al. 2008).Maximum-likelihood (ML) approaches classify animals into a limited number of relationship classes (Mousseau et al. 1998; Thomas et al. 2002; Wang 2004; Herbinger et al. 2006; Anderson and Weir 2007). For each pair a likelihood to fall into a possible relatedness class (e.g., full sib vs. unrelated) is calculated given its genotype and phenotype. ML techniques combined with a Markov chain Monte Carlo approach reconstruct groups with specific relationships jointly and are therefore more efficient than other ML approaches. To minimize standard errors, all discussed ML methods require balanced population structures, large sibling groups, and a large variance of relatedness (Thomas et al. 2002; Wang 2004; Anderson and Weir 2007). Therefore, these methods may not be suitable for natural mating systems.Unlike parental allocation methods, a benefit from relatedness estimators is that essentially all selection candidates are maintained for breeding value estimation, even with missing parents. The question is, however, whether such relatedness estimators also give accurate breeding values to perform selection.In this study, we test suitability of a relatedness estimator to obtain breeding values in a population of common sole, Solea solea (n = 1953) obtained by natural mating. First, we estimate breeding values using pedigree relatedness of animals for which a pedigree could be reconstructed (using parental allocation). This data set (n = 1338) is further referred to as “reduced data set.” We compare results with estimated breeding values using a simple but robust method-of-moments relatedness estimator: “molecular relatedness” (Toro et al. 2002, 2003). Next, we estimate breeding values using molecular relatedness in the full data set (n = 1953). Results show that accuracies of estimated breeding values obtained with molecular relatedness and pedigree relatedness are comparable. Accuracy increases when breeding values are estimated with molecular relatedness in the full data set. This implies that a molecular relatedness estimator can be used to estimate breeding values in captive natural mating populations.     

Energy Content of Antarctic Mesopelagic Fishes: Implications for the Marine Food Web

For a better understanding of the role of mesopelagic fish in the Southern Ocean food web, the energy and water content of Bathylagus antarcticus, Electrona antarctica and Gymnoscopelus braueri from the Lazarev Sea were investigated. Mean dry weight energy content of B. antarcticus (20.4 kJ g⁻¹) was significantly lower than in E. antarctica and G. braueri (both 29.4 kJ g⁻¹). In E. antarctica, an increase of dry weight energy density with age was evident from 26.9 kJ g⁻¹ in juveniles of less than 1 year of age to 32.0 kJ g⁻¹ in 3-year-old fish. Water content decreased with size in all three species. Abundant high-energy species such as E. antarctica are at a key position in the food web. Due to a marked influence of age on energy content, population structure can be an important variable in estimates of energy fluxes in the Southern Ocean ecosystem.     

Viral nanoparticles as tools for intravital vascular imaging

A significant impediment to the widespread use of noninvasive in vivo vascular imaging techniques is the current lack of suitable intravital imaging probes. We describe here a new strategy to use viral nanoparticles as a platform for the multivalent display of fluorescent dyes to image tissues deep inside living organisms. The bioavailable cowpea mosaic virus (CPMV) can be fluorescently labeled to high densities with no measurable quenching, resulting in exceptionally bright particles with in vivo dispersion properties that allow high-resolution intravital imaging of vascular endothelium for periods of at least 72 h. We show that CPMV nanoparticles can be used to visualize the vasculature and blood flow in living mouse and chick embryos to a depth of up to 500 microm. Furthermore, we show that the intravital visualization of human fibrosarcoma-mediated tumor angiogenesis using fluorescent CPMV provides a means to identify arterial and venous vessels and to monitor the neovascularization of the tumor microenvironment.     

Skeletal muscle weakness in osteogeneis imperfecta mice

Exercise intolerance, muscle fatigue and weakness are often-reported, little-investigated concerns of patients with osteogenesis imperfecta (OI). OI is a heritable connective tissue disorder hallmarked by bone fragility resulting primarily from dominant mutations in the proα1(I) or proα2(I) collagen genes and the recently discovered recessive mutations in post-translational modifying proteins of type I collagen. In this study we examined the soleus (S), plantaris (P), gastrocnemius (G), tibialis anterior (TA) and quadriceps (Q) muscles of mice expressing mild (+/oim) and moderately severe (oim/oim) OI for evidence of inherent muscle pathology. In particular, muscle weight, fiber cross-sectional area (CSA), fiber type, fiber histomorphology, fibrillar collagen content, absolute, relative and specific peak tetanic force (P_o, P_o/mg and P_o/CSA respectively) of individual muscles were evaluated. Oim/oim mouse muscles were generally smaller, contained less fibrillar collagen, had decreased P_o and an inability to sustain P_o for the 300-ms testing duration for specific muscles; +/oim mice had a similar but milder skeletal muscle phenotype. +/oim mice had mild weakness of specific muscles but were less affected than their oim/oim counterparts which demonstrated readily apparent skeletal muscle pathology. Therefore muscle weakness in oim mice reflects inherent skeletal muscle pathology.     

Single amino acid mutations in the Saccharomyces cerevisiae rhomboid peptidase,Pcp1p,alter mitochondrial morphology

Key to mitochondrial activities is the maintenance of mitochondrial morphology, specifically cristae structures formed by the invagination of the inner membrane that are enriched in proteins of the electron transport chain. In Saccharomyces cerevisiae , these cristae folds are a result of the membrane fusion activities of Mgm1p and the membrane‐bending properties of adenosine triphosphate (ATP) synthase oligomerization. An additional protein linked to mitochondrial morphology is Pcp1p, a serine protease responsible for the proteolytic processing of Mgm1p. Here, we have used hydroxylamine‐based random mutagenesis to identify amino acids important for Pcp1p peptidase activity. Using this approach we have isolated five single amino acid mutants that exhibit respiratory growth defects that correlate with loss of mitochondrial genome stability. Reduced Pcp1p protease activity was confirmed by immunoblotting with the accumulation of improperly processed Mgm1p. Ultra‐structural analysis of mitochondrial morphology in these mutants found a varying degree of defects in cristae organization. However, not all of the mutants presented with decreased ATP synthase complex assembly as determined by blue native polyacrylamide gel electrophoresis. Together, these data suggest that there is a threshold level of processed Mgm1p required to maintain ATP synthase super‐complex assembly and mitochondrial cristae organization.     

Metabolic Implications of Exposure to Light at Night: Lessons from Animal and Human Studies

Lately, the incidence of overweight, obesity, and type 2 diabetes has shown a staggering increase. To prevent and treat these conditions, one must look at their etiology. As life on earth has evolved under the conditions of nature’s 24‐hour light/dark cycle, it seems likely that exposure to artificial light at night (LAN) would affect physiology. Indeed, ample evidence has shown that LAN impacts many metabolic parameters, at least partly via the biological clock in the suprachiasmatic nucleus of the hypothalamus. This review focuses on the impact of chronic and acute effects of LAN of different wavelengths on locomotor activity, food intake, the sleep/wake cycle, body temperature, melatonin, glucocorticoids, and glucose and lipid metabolism. While chronic LAN disturbs daily rhythms in these parameters, experiments using short‐term LAN exposure also have shown acute negative effects in metabolically active peripheral tissues. Experiments using LAN of different wavelengths not only have indicated an important role for melanopsin, the photopigment found in intrinsically photosensitive retinal ganglion cells, but also provided evidence that each wavelength may have a specific impact on energy metabolism. Importantly, exposure to LAN has been shown to impact glucose homeostasis also in humans and to be associated with an increased incidence of overweight, obesity, and atherosclerosis.     

Neuropeptide changes in the suprachiasmatic nucleus are associated with the development of hypertension

ABSTRACT

Human postmortem studies as well as experimental animal studies indicate profound changes in neuropeptide expression in the suprachiasmatic nucleus (SCN) in several pathological conditions including hypertension. In addition, animal experimental observations show that the SCN peptides, vasopressin (AVP) and vasoactive intestinal peptide (VIP) are essential for adequate rhythmicity. These data prompted us to investigate whether changes in these neuronal populations could be the cause or consequence of hypertension. Changes in blood pressure and levels of neuropeptide expression in the SCN were determined during development of hypertension in spontaneously hypertensive rats (SHR), in 2K1C reno-vascular induced hypertensive animals and their respective controls. During the pre-hypertensive stage (5 weeks of age), the VIP and AVP content was higher and the somatostatin (SOM) content was lower in the SHR SCN. At the onset of hypertension (12 weeks of age), when blood pressure levels had just reached about 140 mmHg, AVP and SOM content in the SCN was not different anymore in SHRs compared to control, but VIP was still higher. After 16 weeks, the AVP content was decreased, but SOM was increased and the overall level of VIP in the SCN was still higher in SHRs compared to controls. None of the aforementioned changes in the SCN was observed after induction of hypertension in the 2K1C model. However, while VIP was increased in the NTS projecting medial region of the SCN in SHR animals only after the establishment of hypertension, VIP was decreased in the same region in the 2K1C induced hypertensive rats. Consequently, the present findings confirm previous studies in human and rat indicating that changes in the SCN are strongly associated with the development of hypertension. In addition, the changes in peptide content in the 2K1C animals indicate that the SCN is also able to respond to increases in blood pressure.     

High-throughput SNP discovery and genotyping in durum wheat (<Emphasis Type="Italic">Triticum durum</Emphasis> Desf.)

We describe the application of complexity reduction of polymorphic sequences (CRoPS^®) technology for the discovery of SNP markers in tetraploid durum wheat (Triticum durum Desf.). A next-generation sequencing experiment was carried out on reduced representation libraries obtained from four durum cultivars. SNP validation and minor allele frequency (MAF) estimate were carried out on a panel of 12 cultivars, and the feasibility of genotyping these SNPs in segregating populations was tested using the Illumina Golden Gate (GG) technology. A total of 2,659 SNPs were identified on 1,206 consensus sequences. Among the 768 SNPs that were chosen irrespective of their genomic repetitiveness level and assayed on the Illumina BeadExpress genotyping system, 275 (35.8%) SNPs matched the expected genotypes observed in the SNP discovery phase. MAF data indicated that the overall SNP informativeness was high: a total of 196 (71.3%) SNPs had MAF >0.2, of which 76 (27.6%) showed MAF >0.4. Of these SNPs, 157 were mapped in one of two mapping populations (Meridiano × Claudio and Colosseo × Lloyd) and integrated into a common genetic map. Despite the relatively low genotyping efficiency of the GG assay, the validated CRoPS-derived SNPs showed valuable features for genomics and breeding applications such as a uniform distribution across the wheat genome, a prevailing single-locus codominant nature and a high polymorphism. Here, we report a new set of 275 highly robust genome-wide Triticum SNPs that are readily available for breeding purposes.     

Plasma lecithin:cholesterol acyltransferase and carotid intima-media thickness in European individuals at high cardiovascular risk

Lecithin:cholesterol acyltransferase (LCAT) is the enzyme responsible for cholesterol esterification in plasma. LCAT is a major factor in HDL remodeling and metabolism, and it has long been believed to play a critical role in macrophage reverse cholesterol transport (RCT). The effect of LCAT on human atherogenesis is still controversial. In the present study, the plasma LCAT concentration was measured in all subjects (n = 540) not on drug treatment at the time of enrollment in the multicenter, longitudinal, observational IMPROVE study. Mean and maximum intima-media thickness (IMT) of the whole carotid tree was measured by B-mode ultrasonography in all subjects. In the entire cohort, LCAT quartiles were not associated with carotid mean and maximum IMT (P for trend 0.95 and 0.18, respectively), also after adjustment for age, gender, HDL-cholesterol (HDL-C), and triglycerides. No association between carotid IMT and LCAT quartiles was observed in men (P=0.30 and P=0.99 for mean and maximum IMT, respectively), whereas carotid IMT increased with LCAT quartiles in women (P for trend 0.14 and 0.019 for mean and maximum IMT, respectively). The present findings support the concept that LCAT is not required for an efficient reverse cholesterol transport and that a low plasma LCAT concentration and activity is not associated with increased atherosclerosis.